Ewan Birney


Bio::SearchIO::Writer::HTMLResultWriter - Object to implement writing a Bio::Search::ResultI in HTML.


  use Bio::SearchIO;
  use Bio::SearchIO::Writer::HTMLResultWriter;

  my $in = new Bio::SearchIO(-format => 'blast',
                             -file   => shift @ARGV);

  my $writer = new Bio::SearchIO::Writer::HTMLResultWriter();
  my $out = new Bio::SearchIO(-writer => $writer);


This object implements the SearchWriterI interface which will produce a set of HTML for a specific Bio::Search::Report::ReportI interface.


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AUTHOR - Jason Stajich

Email jason@bioperl.org

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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _


 Title   : new
 Usage   : my $obj = new Bio::SearchIO::Writer::HTMLResultWriter();
 Function: Builds a new Bio::SearchIO::Writer::HTMLResultWriter object 
 Returns : Bio::SearchIO::Writer::HTMLResultWriter
 Args    :


 Title   : remote_database_url
 Usage   : $obj->remote_database_url($type,$newval)
 Function: This should return or set a string that contains a %s which can be
           filled in with sprintf.
 Returns : value of remote_database_url
 Args    : $type - 'PROTEIN' or 'P' for protein URLS
                   'NUCLEOTIDE' or 'N' for nucleotide URLS
           $value - new value to set [optional]


 Purpose   : Produces data for each Search::Result::ResultI in a string.
           : This is an abstract method. For some useful implementations,
           : see ResultTableWriter.pm, HitTableWriter.pm, 
           : and HSPTableWriter.pm.
 Usage     : print $writer->to_string( $result_obj, @args );
 Argument  : $result_obj = A Bio::Search::Result::ResultI object
           : @args = any additional arguments used by your implementation.
 Returns   : String containing data for each search Result or any of its
           : sub-objects (Hits and HSPs).
 Throws    : n/a


  Title   : id_parser
  Usage   : $index->id_parser( CODE )
  Function: Stores or returns the code used by record_id to
            parse the ID for record from a string.  Useful
            for (for instance) specifying a different
            parser for different flavours of FASTA file. 
            Returns \&default_id_parser (see below) if not
            set. If you supply your own id_parser
            subroutine, then it should expect a fasta
            description line.  An entry will be added to
            the index for each string in the list returned.
  Example : $index->id_parser( \&my_id_parser )
  Returns : ref to CODE if called without arguments
  Args    : CODE


  Title   : default_id_parser
  Usage   : $id = default_id_parser( $header )
  Function: The default Fasta ID parser for Fasta.pm
            Returns $1 from applying the regexp /^>\s*(\S+)/
            to $header.
  Returns : ID string
  Args    : a fasta header line string